Helpless Aggression
by sapphireshimmer2010
Summary: On a lone Replicator ship found in space, John finds a surprise that may crush his heart. Post BAMSR. So SPOILERS for a lot of season 4.
1. Chapter 1

AN (sparklyshimmer): Me and my sis have finally finished a chapter for a long-planned joint fic!! Hooray!! Ok, this idea came from the ending of BAMSR, I think everyone will rather enjoy it, I take credit for most of this chapter, but my sis gets her stuff in very soon. :)

A/N (saphire): Sparkly did write pretty much this whole chapter with some input from me. She told me her idea that she got and I loved it! So anyway, hope you enjoy. Please review:)

* * *

"I still think Ronon is a good name for a boy or girl." Ronon grinned at Teyla across from him. The team plus Doctor Keller sat in the mess hall.

John made a face. "For a girl?"

"Yeah. Why not?"

"Oh please. That is not a girl's name. But if you're going to name your baby after anyone, Rodney is the name of a brilliant man destined for greatness." said the scientist and added, "And if it's a girl, well then I guess there's always Meredith."

"Of course, Rodney." She smiled at them all with laughter in her eyes.

"I've always like the name Emily." Keller spoke up.

Just then John got a call through his radio from Carter.

"Colonel Sheppard? I need you down in the control room immediately."

"On my way."

The team got up and headed off, Ronon excusing himself from Keller and giving her a soft smile. As soon as they got to the control room John noticed Major Lorne's team talking to Carter with serious expressions. He walked over to them with Ronon, Rodney, and Teyla following close behind.

"Major. Colonel." John greeted the two of them.

"John, good. We have some news."

Before she continued, Rodney let out a groan. They all looked at him.

"Good news or bad news?"

"Well it's not good news." Said one of Lorne's men, a young Lieutenant.

Everyone turned their attention to him. "What?" he shrugged.

Sam turned back to John. "Looks like we missed a replicator ship." She said.

"What?!"

"Excuse me?!"

Rodney and John looked at her incredulously. Ronon and Teyla both looked surprised. Lorne explained to them. "My team was on a routine mission, dropping in for a chat with one of our trading partners. We took a jumper and long range sensors showed a replicator ship. It wasn't moving."

"Did we not destroy them all?" Teyla asked. "How is this possible?"

"It shouldn't be." Rodney interrupted Sam as she started to speak. "The scans indicated that all the ships had been pulled in to the Asuran planet."

"Well maybe one ship wasn't close enough to be pulled in." John suggested.

"Then the device the other us gave us should have showed it."

"However it got there, I say we destroy it." This comment from Ronon surprised no one.

"Ronon's right. We'll have to get the Daedalus or Apollo back to Atlantis as fast as possible."

John looked over at Sam uncertainly. She noticed.

"You disagree Colonel?"

"I was just thinking. Why is there just one ship out there? Shouldn't there be more by now?"

Sam didn't say anything, instead averting her gaze and thinking.

"I just have a feeling." John continued. "Let my team take a jumper to check it out, maybe figure out what they're doing."

"Are you planning on sneaking aboard? Because I will not approve this mission if that's the case." She said, somewhat sharply.

"We don't have to get on board. We can cloak and fly by and Rodney can do some scans. Assess if they have any damage, see if I can pick up on anything else."

She sighed. "All right. If you don't get anything within one to two hours, you fly straight back." She told them sternly.

John nodded.

"Ok Colonel. You leave in an hour." She headed for her office.

* * *

The three guys were gearing up when Teyla walked in. "Ronon? You are going?" she asked. 

"Yeah. I've been gettin' bored. Want to do something." He saw the look on her face, knowing that she would very well have nothing to do there either. "Sorry." He added.

"You're not here to convince me to let you come with us are you?" John asked.

"No." she smiled. "I am not. I merely came to wish you good luck."

John nodded and smiled back. "All right kids, let's go."

The three left, Rodney complaining along the way about being rushed.

* * *

"You getting anything Rodney?" John asked. 

Rodney looked at his hand held tablet and then checked some readings behind him in the jumper. He sighed. "No. Nothing."

"Well we've still got some time to kill. Maybe we arrived just in time for the party."

As if on cue, the jumper was fired on.

"What the hell?! Rodney I thought we were out of their sensor range?"

"We _are!_ That didn't come from the replicator ship." Rodney frantically looked at his readings.

"Then where did it come from?" Ronon asked.

"I don't know, but we are getting out of here." John tried to fly away but nothing happened other than more hits to the jumper. They all held on to the nearest surface trying not to be jolted out of their seats. "Rodney! Why can't I go anywhere? And why can't I fire back?"

"Because both turning and weapon controls were damaged."

"Well fix it!"

"It's not that simple, Sheppard. Whoever's shooting at us knew just where to hit us!"

Just then another jumper decloaked in front of them. They stared at it in surprise.

"Please tell me that's not the replicators McKay."

"Can't do that. They're sending us a message." Rodney said. "Huh." John looked at McKay. "The, uh, replicator ship is going to fly to us and we can fly straight into the jumper bay."

"Well I guess we don't have much of a choice. We're not going anywhere."

"Great." Said Ronon, in a way that couldn't be said if it was sarcastic or not. "Maybe now we can destroy it."

"Who knows? Maybe." Said John.

* * *

John stopped the jumper and they stood up. 

"Now what?" asked Rodney.

Ronon took his gun out and John prepared his. "Oh, do you seriously think they're going to let us keep our weapons?"

"Of course not, Rodney, but _we're _not going to let them capture us. Ok?"

Before any of them could do anything the back door to the jumper opened to reveal several replicators with their stun guns. They immediately shot Ronon and John.

"Oh yeah, we won't get caught." Rodney muttered sarcastically. He held his hands up in the air, showing he had no weapons, but the replicators shot him unconscious as well.

* * *

The first thing John saw when he woke up was the black inside of a blindfold tied around his head. As he went to move his arms to take it off, he found that – of course – they were tied up. _Damn those replicators, _he thought. 

"Ronon? Rodney? You guys there?" He called quietly.

"I'm here." Came Ronon's voice.

Rodney groaned as he came to. "What happened? Where are we? Oh no, I can't see anything!"

"You're blindfolded McKay." Ronon gruffly informed the panicking scientist.

"Wonderful." John heard Rodney mutter. Then he heard footsteps. A pair of arms grabbed him and pulled him up.

"Uh, hey guys." He was being roughly pushed away. "Mind telling me where we're going?" John asked in his usual flippant way.

"We are taking you to our commander. She has requested your audience." A male voice answered nonchalantly.

"Oh she has, has she?"

They kept moving for a couple of minutes until the replicators shoved him to the ground, face first. He could only imagine the silent, compliant nod they gave their commander. His blindfold was removed and the first things he saw were black boots and a nice pair of leather pants up to the commander's knees. John couldn't resist commenting.

"Well, with an outfit like that, at least my captor is pretty hot."

A laugh caught his ears, and for a moment his heart constricted. _No. It can't be. _But he knew that laugh. He loved to hear that sound. Especially directed at him.

The woman moved closer. He laid there frozen, afraid to look up and see if his saddened mind was playing a trick on him. Afraid to look up in case it was in fact true.

But as soon as her voice flowed smoothly in his ears he looked up sharply. Standing less than five feet away was Elizabeth Weir.

"If you're going to make comments like that, Colonel, I suggest you know who you're talking to."She smirked at John, whose mind was still incapable of gathering his thoughts. "But I'm flattered."

"E – Elizabeth?" He stammered.

"Hello John."


	2. Chapter 2

Chapter 2

Her saying his name let a number of memories fall back into place. He'd tried to forget about her since the news of her death. It had devastated all of Atlantis to lose their leader, but had hit him the hardest of all, having lost the closest friend he cared a lot about. How much so he still wasn't sure, but looking up at her curly brown hair and wonderful green eyes, every feeling for her came rushing back. Happy, angry, worried, sad, all cascading down and encircling him.

He stood up, struggling a little since his hands were still tied behind his back, and continued to stare at her. _Was it really his – their – Elizabeth, or just another copy?_

She stood with her arms crossed, leaning with most of her weight on her left foot. She looked amused.

"Are you going to just stare at me, Colonel?" she asked.

John cast away his thoughts. "You're in charge of a replicator ship?!"

She looked downwards. "I'm still good, John."

He wasn't entirely sure about that, though he desperately wanted to believe it. "They told us you were dead." he spoke softly, voice heavy with emotion.

When he said this she looked up sharply, immediately realizing what he was thinking. "It's me. I'm half-replicator, taken by Oberoth in our mission to get a ZPM. But I escaped from him with a faction of Asurans."

John's eyes widened a little. The last time they had not given her her full memory. And why would Oberoth make a copy of her? _It's really her, _he thought. _It's really __my – our – Elizabeth_. Though he wasn't entirely sure if it was a good thing as of that moment. At least there was hope now that they could bring her back home.

He had the urge to hug her, to touch her, but the look she now possessed stopped him.

"I'm glad you finally found us. I was beginning to get a little impatient. I was hoping you wouldn't just shoot us down. Sorry about your jumper, but I need your help."

He stared at Elizabeth somewhat disbelievingly. "You sat around here so we would come by so you could talk to us?""Yes. So?" She raised an eyebrow at him in the typical Elizabeth Weir fashion and he realized how much he missed that about her. Hell, he missed pretty much everything about her.

"'So?' Why'd you have to knock us out, blindfold us, and tie us up? Speaking of which, do you think you could untie my arms?"

She gave him a crooked smile. "Sorry John, I can't do that. And to answer your first question, well, I thought it'd be more fun."

"You thought it'd be more _fun?"_He gave her a look, a mixture of annoyance, disbelief, and amusement.

"Okay," he said slowly, drawing it out into two distinct syllables. "What do you need to talk about?"

Elizabeth became serious. "I need your help with a little project of mine."

"And what would that be?"

"Let's make a deal. I'll answer your questions after you answer a few of mine."

John hesitated. He wanted to know what Elizabeth was planning, but he also knew that he couldn't tell her anything important about Atlantis. "Ok." He finally said.

"Good. First one. I'm curious. Where's Teyla? I expected her to be in the jumper too."

"She's not on my team right now." He sounded slightly bitter.

She looked confused. "Why not?"

"Because she's pregnant."

Shock showed on Elizabeth's face for a brief moment before a soft, somewhat sad smile graced her lips. "Well you'll have to tell her congratulations for me.""Why? Are you going to let us go home?"

"Eventually. Who's the father?"

"Kanan."

"Athosian?" she guessed.

"Yes."Elizabeth thought she understood the bitterness now. She had always noticed a connection between Teyla and John. She figured that he must be jealous.

"Now," John continued. "My turn for a question."

"Wait. I've got more first. How is everyone else?"

"They're good."

"What about Keller? Is she head of medical staff?"

"Yeah. Doing a pretty good job, too. Between you and me, I think there's something between her and Ronon."

"Oh?"

"Yeah. Something definitely happened with them during that quarantine lockdown."

"Quarantine lockdown?"

"Yeah. I probably shouldn't have mentioned that."

"Who replaced me?"

"Colonel Samantha Carter."

Elizabeth grimaced, something that didn't escape John's attention. Though he noticed she didn't look particularly surprised that a military personnel was now in charge. "Don't like her?"

"Well, Colonel Carter and I didn't exactly see eye to eye when I worked at the SGC. How is she doing as leader?"

"She's doing a pretty good job." He admitted.

"Did you find a good planet to land Atlantis on?"

"Ye – es." He dragged out the word into two syllables, deciding that it was ok to tell her that small detail.

"How did you get rid of the replicators?"

John kept quiet and she sighed. She had known he probably wouldn't tell her that. "So who told you I was dead?" Her voice softened.

Pain appeared in his eyes but it was gone instantly. So instantly that Elizabeth wasn't actually sure if it had even been there. Then she couldn't read his expression at all.

"A group of replicators who made a fake Atlantis."

"A fake Atlantis?"

"Yeah. We came across another set of us. It was kinda creepy."

"So what did you do with my stuff?"

"We sent it all back to Earth. Your mother has it now." The pain was back in the eyes that matched her own and he had a faraway look on his face as if he was remembering something.

Flashback

_John took a deep breath and rang the doorbell. A large cardboard box sat next to him on the front porch. The door to the small white house opened. A woman in her fifties was inside. She smiled but the smile disappeared a second later when she got a good look at him._

_John knew she must be thinking the worst seeing him in his dress blues. Unfortunately, the woman was right to be thinking the worst._

_Then the woman's eyes fell on the box. "Oh my God." Her hand flew to her mouth and tears started to form in her eyes._

_"Mrs. Weir, I'm John Sheppard. I worked with Elizabeth." He had purposely left out his rank. The dress blues were bad enough. "Could I come in?"_

_Mrs. Weir didn't say anything. She just moved aside to let him pass. John picked up the box and stepped through the doorway. He was led to the family room, where he set the box down on the coffee table.__ She motioned him to take a seat on the couch while she sat across from him in an armchair._

_John didn't know where to begin, but he didn't have to when she asked, "Is my daughter dead, Mr. Sheppard?" It was almost a whisper._

_He had been trying to stay comp__osed for Elizabeth's mother, but he knew some emotion was visible. "That's what we've been told, Mrs. Weir."_

_There was something in his tone __that__made her ask, "But you don't believe that?"_

_"I'm not sure. I don't want to."_

_"Can you tell me what happened?"_

_"I'm sorry, ma'am. It's classified."__She just nodded and he knew that she hadn't really been expecting an answer. With trembling hands, Mrs. Weir reached into the box and pulled out one of the items in it. It was a silver pocket watch. The one that John had seen her holding several times – particularly after the time the nanites had invaded her body._

_Elizabeth's mother stared at it for a few seconds before setting it down next to the box on the table. She then repeat__ed the process with several mo__r__e__ of Elizabeth's possessions. "You said you worked with Elizabeth?"__"Yes. She was my boss."__An eyebrow lifted and John immediately knew where Elizabeth ha__d inherited her expression from. "How was my daughter the boss of a military man?"_

_"Well, it is mainly a scientific expedition and they wanted a civilian in charge."_

_She nodded, not bothering to ask who 'they' was. "Elizabeth sent a few letters home during the last three years. She always mentioned you in them. Seemed like the two of you were close."__The corners of John's lips curved upward in a small smile, despite his mood, upon hearing that Elizabeth had mentioned him in her letters to home. "Yeah. She was pretty much my best friend."__From the look in his eyes, Mrs. Weir was pretty sure that he cared about her daughter as more, but didn't say anything. "Then I want to thank you for coming down here personally.__"_

_John was quiet. Then Mrs. Weir withdrew a ceramic pot from the box. She examined it for a minute. "I gave that to Elizabeth for her birthday." He told her._

_"Then you should be the one to keep it." She placed it in front of him. "I know she would want you to have it."_

_He reached a hand forward and grabbed it. He held it, remembering that day. "Thank you."__It was silent again for a few moments while she continued to look at all of Elizabeth's things. John finally stood up, saying, "Well, I should be going Mrs. Weir. I am truly sorry about Elizabeth."_

_She nodded and walked with him to the door. "Thank you for coming." He nodded too and then left._

End Flashback

Elizabeth didn't respond to his answer. So he took advantage of the silence. "My turn to ask questions now."

She sighed. "Alright, what would you like to know first?"

"Uh…how have you been doing? You know, in the last year.." Concern was clear in his voice as he trailed off a little awkwardly. This question wasn't quite the one she imagined would come first and she was touched by it.

"It was tough in the beginning," she admitted. "But I'm fine now."

"What do you mean 'it was rough in the beginning'," he demanded. "What did they do to you?"

"It doesn't matter." She avoided his eyes.

John was starting to get annoyed and frustrated. Sometimes during their conversation she seemed like the old Elizabeth Weir. The one he knew. But then at other times, she was unfamiliar to him – not telling him anything at all. He wasn't used to that from her.

"Of course it matters! What did they do to you?"

She didn't answer, staring off to her right.

"Elizabeth!"

She ignored him, clearly not wanting to talk about it. "Dolan, please take him back to the cell." She then turned away from him.

John felt two hands roughly grab him from behind. He didn't struggle and let himself be pushed out of the room. He was too busy thinking. He knew that Oberoth must have done something really horrible to her to make her react like that. And he wondered what it was.


	3. Chapter 3

**A/N (saphire): **First off thanks to Lantia4ever, Charmed225, and JenniDinoRobot for reviewing the last chapter! We were a little disappointed to only get 3 reviews though when we have quite a few alterts, so please r & r! Well, here's the 3rd chapter (written mainly by shimmer). Hope you like it!

**AN (sparkly): **So many thanks for all the reviews and alerts! Heres the next chapter, enjoy! Please review and tell us what you like!

Chapter 3

The replicator – Dolan – threw John back into the cell. He stumbled in and sat up. He noticed that Rodney and Ronon's blindfolds had been removed, though all three of them were still tied up. Ronon glared fiercely at the men as they left.

"You OK?" asked Rodney nervously, afraid of the answer.

"Yeah, I'm fine." John answered, though truthfully his insides were in turmoil.

"Where'd they take you?" asked Ronon.

John couldn't answer. He just stared hard at the floor, jaw set, eyes clouded.

"Sheppard?" Ronon prompted.

"They took me to Elizabeth." He finally gave up quietly.

"Uh, I'm sorry what?" Rodney asked, "because I thought you just said they took you to Elizabeth, as in our friend and old leader, and given the fact that she is dead right now, I don't see how that's possible." He rambled, needing to understand but unaware of how the harsh words hit his friend.

"That's what I said Rodney." He stated simply, "And it's true."

"How?" Ronon asked.

John shook his head, still in some disbelief. "She's their leader."

Ronon took on an angry look as Rodney exclaimed aloud, "What!?"

"She…After we left the Asuran planet, they did _something_ to her, but she escaped with some of them. They made her their leader and whatever they've been doing, they need our help." As he spoke he found it hard to keep his voice strong.

"So – so she's alive?"

"Yes Rodney, she's here."

"Huh." Rodney smiled slightly. "Well then, that's good, right?"

"I don't know Rodney. I'm not sure we'll be able to get her back. At least not right away."

"Oh." His voice and face fell and the three men lapsed into a suffocating silence. But soon enough the sound of voices drifted to them, breaking their thoughts. Four replicators came in front of the cell, following Elizabeth.

Rodney and Ronon sat up straight immediately after seeing her. Though John had told them, it was still a shock that almost shattered their bones.

She stepped lightly up to the bars as they opened and stepped in. she smiled at them, lingering on Ronon and Rodney. "Hello boys." The three stood up.

"Hi." Ronon grunted.

Rodney looked at him. "Yeah, uh, hi."

"So Elizabeth, are you gonna tell us what you have planned? Why we're here…what you want us to do…anything?"

"We found a weapon, Ancient design, on a planet. We know it will help in our fight against the wraith. It will cause serious damage."

"Sounds nice."

She smiled sarcastically at John. He was still the same. Perhaps his eyes were a bit more bitter and haunted than when they'd last seen each other, but he hid it well beneath his attitude.

"The weapon won't work. And although we have scientists aboard, we can't get it to work." She turned to McKay. "So we want you to help us fix it."

"Well-" Before Rodney could finish the thought, John cut him off.

"And what if we don't?" he gazed steadily at her. As much as he wanted to do this, to have a weapon against the wraith, to try and get Elizabeth back, he knew they couldn't just agree to it.

She turned to look at him again, and this time his eyes widened at her demeanor. She gave the appearance of authority as coldness radiated from her eyes. The reminiscent smile was gone, leaving a harsh frown in its place. John just stared, trying to make sense of this new, very different Elizabeth.

"Sorry Colonel?" she asked, though knowing full well what he had said.

"Do you really think we're just going to help you?"

"This isn't exactly a choice for you." Her voice authorized no argument in its iciness.

The three stuck in the cell remained quiet so she continued. "If you all want to get back home, I suggest you fix this weapon." She nodded to the men who had come with her and thus far done nothing but watch approvingly. Two of them took their weapons out and aimed them at John and Ronon. The other two grabbed Rodney's arms, who started to panic.

"Hey, what are you doing?"

Her voice softer now, but still rather emotionless, she said, "You are going to come with me." With that she turned and left, McKay being pushed after her. Ronon glared and practically growled at the replicators that were left. As soon as Elizabeth and Rodney were out of view they left.

Ronon and John sat back on the floor again, another silence approaching.

* * *

"Are you finished yet?" Elizabeth demanded as she came into the Jumper where Rodney was working, guarded by a replicator named Huron.

Rodney glanced at her uncomfortably. She was disconcerting this way, a leader that didn't always care, just wanted the job done. Similar to how she was when Phoebus had occupied her mind. Except that this was her... she wasn't possessed, she just wasn't her _usual _self…

He gave himself a mental shake and let it go. It was confusing to think about. But no matter what kind of state she put him in, he was still going to answer with his annoyance obvious.

"You think I can have this damage fixed in less than half an hour!? And with this guy here with a weapon five feet from my chest!?"

She eyed him sharply. "How much longer then?"

He sighed. "Twenty minutes tops."

"Good. Thank you Rodney."

"Right. At least you untied me." He mumbled.

He watched her leave then turned back to the controls.

* * *

About forty minutes after Elizabeth had left, she strode back up to the cell with Dolan.

"Where's McKay?" Ronon said, sounding threatening.

"He's fine." She nodded to him.

"Look Elizabeth, what do you want us to do? Sure McKay is good, but you have no idea if he can fix this weapon."

"He's going to at least try. I have faith in him."

"Well he doesn't have any equipment with him. How do you expect-"

She cut him off. "Which is why you will be going back to Atlantis to get whatever he needs."

John tilted his head at her. "Ok, sure. When do we leave?"

She smiled and raised an eyebrow at him. "You leave right now Colonel."

She moved aside and Dolan opened the cell. John stepped out cautiously. Ronon walked forwards, but Elizabeth stopped him with a hand up. She glanced apologetically at John.

"I'm sorry, but you misunderstood me. John and Rodney will be leaving. Ronon, you're staying here."

John groaned inwardly. Of course! Ronon for his part tried to fight his way out, but his arms were still confined behind his back and while Dolan had his weapon trained on John, Elizabeth took out one of her own and stunned Ronon quickly.

John stared in shock at her once again. She lowered her arm and locked eyes with him. Confusingly, he saw her eyes looked sad, agitated.

John looked away.

"Let's go." she commanded.

* * *

"Sheppard!" Rodney exclaimed. "Where's Ronon?"

"He's not coming."

"What?"

"They're letting us go back to Atlantis so you can get equipment. Ronon is Elizabeth's way of making sure we come back."

"Damn."

"Yeah." Huron stepped out of the jumper and John moved near Elizabeth.

"Tell Sam you'll be with us for about a week. I want you back in at least six hours."

"And if we aren't?"

"Don't test me Colonel." Her face was very stern, but other than that unreadable. He wasn't sure he'd be able to read her at all while McKay worked on the weapon. "I know you'll come back in that time. You're not leaving Ronon. You didn't the last time."

She was right. Ronon was his family and a member of Atlantis. He would do anything for him. And he wasn't leaving her either.

"And don't come with more than Rodney and yourself."

John nodded and looked at Huron. Elizabeth gestured for him to leave. Then they were alone as Rodney stood in the jumper looking slightly impatient, but understanding John's need to talk to her. She looked down.

"Look, John, I'm sorry for doing this."

He remained silent, having nothing he could possibly say. All he wanted to do was crush himself to her smaller body in a comforting hug. But he didn't dare. Her behavior left it unclear as to whether or not it would be acceptable. One minute she was aggressive and the next the compassionate woman he knew.

"I just want to get this weapon online. And then if you let us we'll leave you alone." Pain stabbed John's heart at the thought of losing Elizabeth again. If they _did _bring her back though, they'd be handing her right over to the IOA. God this was a mess.

"Well, I don't mind killing some wraith." He felt the need to reassure her."So I guess I'll be seeing you soon." She smiled and took a step back from their rather close proximity. Neither had noticed.

"See you then." She said.

John hesitated. "I…I'm trusting you Elizabeth." He turned and went into the jumper glancing back once before the door shut. He wasn't sure, but he swore he saw tears start to roll down her cheeks. Despite what was happening, he _did_ still trust her. Somewhere in there she was still Elizabeth.

"Sheppard?" Rodney asked, pulling John from his thoughts as he just stared at the back of the ship. "Are you alright?"

"Fine, McKay." He responded. "Let's get out of here. We have an interesting debriefing ahead of us."


	4. Chapter 4

A/N (shimmer): Hello! Sorry we took a little longer updating this chapter, but here it is! Enjoy, and please review! let us know what you think.

A/N (saphire): I must take full responsibility for the amount of time this has taken to post. It was my part that needed to be written. Anyway, very special thanks to everyone who reviewed and please keep on telling us what you think. Hope you enjoy this chapter!

Ronon blinked his eyes slowly, trying to remember the cause for him being unconscious on the floor of the cell. As soon as the memory hit he jumped to his feet. He walked to the door and stood in front menacingly.

"Hey!" he yelled out. "Anyone there?"

A voice from behind startled him. "Why don't you turn around?" it asked. Ronon spun to face the spot in the corner he had failed to look at.

"Are Sheppard and McKay all right?"

"They're fine Ronon. I don't want to hurt them." Elizabeth said it softly and he couldn't help but believe her. He supposed it only made sense for them to get back to Atlantis anyway.

"I don't want to hurt you either, Ronon." she continued. "Sorry I stunned you."

He just tilted his head slightly to the left. "Not the first time you've shot me."

She raised an eyebrow. "No, I guess not." She thought back to the incident. It had been Phoebus who'd shot him, but still her hands. She'd felt horrible for not being able to prevent it. _Just like all the other things I couldn't prevent from happening, _she thought and suddenly felt an overwhelming sadness.

Ronon noticed that she seemed lost in thought, her eyes somewhat glazed over. "Something you wanted?" he asked. Elizabeth gave her head a small shake and looked at him.

"Well I just figured I didn't know you too well back on Atlantis so I thought maybe we could talk some." She had been leaned back with her back against the wall of the corner, arms crossed. Now she let out a breath and leaned away arms falling down.

Now Ronon raised an eyebrow. "Ok."

She looked away briefly, smiled, and huffed out a small laugh. That was so like Ronon. "What I'm trying to say, Ronon, is I wasn't too sure about you when you first came to Atlantis, but I'm glad you stayed. I… never got a chance to tell everyone that I thought they were great people for coming here. I never got a chance to tell you how grateful I am for all that you've done for us."

Ronon looked down. "Uh. . . You're welcome." he said gruffly then he shrugged. "You guys were killing some wraith. Seemed like a good idea." He smiled.

"Yes. I suppose so." She let out another breath. "Well I suppose I don't need to be here. I'll come back…"

She had the cell door open to leave when Ronon stopped her. "Hey, uh, Dr. Weir?"

She turned slightly. "Yes?"

"Thank you for taking a chance on me." She smiled and nodded. She still hesitated to leave as he seemed to want to say something more.

"You're a good leader." Ronon was silently happy to get the chance to tell her again so she heard. The last time she'd been on the brink of death.

"Thank you." She took a step out, but once again paused as he said one more thing.

"When they come back, it's not just for me."  
Elizabeth bit her lip, deciding not to say that it wasn't likely she would ever be able to go back home to Atlantis. He probably knew it was a possibility anyway. Giving him a sad look, she finally shut the door behind her and walked away.

* * *

The first few minutes in the jumper were silent as they flew towards Atlantis, until Rodney felt he needed to say something. "You know Sam probably won't want you to go back."

John looked at Rodney. "Ronon, a member of my team, is still back there. I'm not leaving him behind, McKay."

"I know. . . But the IOA might pressure her into sending someone else or just scrapping the mission. I mean, Ronon's not from Earth and -"

John interrupted. "Ok, A: the IOA can pressure her all they want, but Elizabeth said not to show up with anyone else. B: It doesn't matter that Ronon's not from Earth. He is still a part of my team, just as much as you and Teyla. And C: Why the hell wouldn't the IOA let me complete this mission, McKay?"

Rodney seemed reluctant to say anything. "McKay?" John was already in a bad mood from everything and he didn't need Rodney adding to his irritation.

"Ok, look. A while ago when I went to go talk to Sam, she was in the middle of a conversation with the IOA and I um, overheard some things that um, I probably shouldn't know."

"Like what?"

"Like the fact that they know you and I were close to Elizabeth and the IOA is worried that if we ever find Elizabeth, we'll do something rash, stupid, outrageous, etcetera, to get her back. If they even approve this mission at all, and I stress the if, then they'll want to send someone like Major Lorne's team who's not so close to her."

John was quiet for a moment while he processed the information. He knew Rodney was right. But none of that was going to stop him from finishing this mission.

"When we reach Atlantis we'll have about four hours before we have to start out again." The rest of the ride was spent in silence.

* * *

"You're late." Sam said. Then she noticed a missing person. "Where's Ronon?"

"Still back on the replicator ship?" John told her.

"What? I thought it was just a fly-by."

"Well, that was the plan."

"All right. You two head down to the infirmary and then we'll debrief. Just come down when you're done." She said, sensing that it wasn't immediately necessary to return for Ronon.

Half an hour later both John and Rodney had been checked out by Keller and they sat in seats across from the Colonel.

"So what happened out there?"

"They had another jumper waiting for us and shot the navigation and weapon controls. We didn't have a choice but to go aboard."

"They were waiting? But how did they even know you were coming?"

"They didn't. They just kinda. . . guessed we would be by."

"So did you steal one of their jumpers to get back?" Sam asked, though she didn't think that was very likely. She knew how loyal Sheppard was. He wouldn't come back without Ronon.

"Not exactly." Rodney spoke up. "They let me fix it and then let Sheppard and I go."

Sam looked surprised. That wasn't exactly normal replicator behavior. "They let you two go but kept Ronon behind?"

"To make sure we go back."

"Why?"

"They want me to help fix a weapon that'll apparently destroy the wraith and they let me go to get whatever I think I might need. But she gave us a time limit and we have a little over three hours before we head back."

"They want you to fix a weapon that they should be able to fix themselves?"

"They're a small group and they do have scientists, but maybe the knowledge was lost to them when they broke away from the collective." John shrugged. Then at Sam's look, "They're another faction that broke away from Oberoth and I think that's why they weren't destroyed. They weren't anywhere near the planet when we imploded it. The difference though between them and our 'clones' is that I don't think they're after ascension. Just getting rid of the wraith."

Sam nodded. "Ok. So who gave you the time limit? I'd like to know the name of whoever we're allying with at the moment."

Both men were silent. "John?" She still got no response from him. "Rodney?" No answer from him either. "Well, obviously you know the name just not giving it to me, so until you tell me, you're not leaving this city." She threatened.

"It was Elizabeth." John said quietly, having put it off long enough.

Sam was shocked. She propped her elbows on the table and put her head in between her hands, rubbing her temples. She already hadn't been looking forward to informing the SGC of this, knowing they didn't particularly like it when enemies became allies – they had put up a huge fuss over Todd. But now Elizabeth was added to the mix. Yep, that was going to be one fun conversation.


	5. Chapter 5

**AN (sparkly): **Ok, so heres chapter 5! Um nothing really to say I guess except once again thanks for the reviews, and enjoy! Sorry though, no sparkyness in this chapter.

**AN (saphire): **First off, thank you to all of you who reviewed! You are awesome. Hope you all like chapter 5 and please keep on reviewing!

Chapter 5

After John and Rodney left, Sam sat for a moment wondering what to do. She had to dial Earth and tell them about the mission. But did she really have to mention Elizabeth? She knew that she _should_, but then they would just be ordered to leave Ronon behind most likely, and there was no way she could do that to John, Rodney, and Teyla.

She sighed. _Why had she even taken this job? _Well, she hadn't exactly had a choice.

A minute later she stood up and walked into the control room, determined to have things go her way. "Dial Earth." She told Chuck. The gate kawooshed and she soon had radio contact with Landry and – unfortunately – Coolidge too.

"Colonel Carter."

"General. Mr. Coolidge." She acknowledged both men and nodded at them through the video feed.

"What can we do for you?" Landry asked.

"Colonel Sheppard's team returned. We've got another rogue group of replicators on our hands, sir."

"I thought you had destroyed them all." Coolidge said.

"So did we." Sam continued to tell them everything John and Rodney had told her. But she had decided not to mention Elizabeth.

"You can't let them go back there," said Coolidge angrily when she finished, "We are already compromised enough!"

"Ronon is still on the ship! And who's to say they won't just come here?"

"Colonel, may I remind you that Ronon is not exactly one of us?" Through her barely controlled anger she registered that Landry sent him a glare.

"And may I remind you, with all due respect, that Ronon helped save your butt and without him you probably wouldn't be here?" That did seem to cause him to think.

"Colonel-"

"They want to use a weapon against the wraith. We can use this to our advantage."

Coolidge sighed. "Do you think you can destroy the replicators when you're done?"

"Maybe…"

He looked at Landry who just shrugged, as if to say yes.

"Then you have a go."

* * *

John stood in the lab, leaning against the wall, out of the way as he watched McKay and Zelenka run around frantically, gathering equipment. Rodney wasn't saying much but Radek kept trying to figure out what exactly was going on. He would ask a question, gaining only a short answer and orders to get something else.

"But what did you find with the replicator ship that you are taking all this equipment back with you?"

"Long story," Rodney replied, "But we're checking out an Ancient machine."

At that moment Teyla walked in. "John?"

He turned to look at her. "Teyla."

She looked at the two harried scientists. "Where is Ronon?"

"Uh, he's still on the replicator ship."

Her eyebrows rose up. "He is what? What did you find?"

"Well that's why I called you down. I wanted to tell you what happened."

She nodded, grateful that he was still keeping her in the loop, and waited for him to continue. When he didn't she laid a hand on his arm. "John? Are you alright? Is Ronon alright?"

John sighed. "Ronon should be fine I think. Uh, see, the ship wasn't abandoned. They were waiting for us. Turns out we have another rouge faction."

Teyla let out a breath. "I see. Then why are you and Rodney back, but Ronon is not?"

"They want us to help them with some kind of Ancient device that could fight some wraith. Ronon was more to stay behind so we'd come back."

Teyla nodded again, remembering her conversation with John from a while back. He'd do anything for his family.

"And we are trusting these replicators?" she asked.

John's face darkened. She almost got caught in the emotion that appeared in his eyes. They always were pretty expressive.

"Elizabeth is their leader." He said simply.

At this Radek stopped what he was doing and stared at the pair near the door. Teyla looked thoroughly shocked and closed her eyes briefly. When she opened them, they looked sad.

"Was it really her, John?"

John remained silent. Yes, she was the Elizabeth he had left on that God forbidden planet, but her question once again caused him to think about how she had acted on the ship.

"Rodney?" Radek asked quietly.

Rodney sighed. "Yes, yes, I will explain, but first we have to go to your lab. I need to get something."

Teyla and John watched the two leave before she turned back to him.

"John. You cannot feel guilty about this-"

"It's really her, Teyla." He cut her off. "It's our Elizabeth. She's not dead."

Teyla smiled softly. "I am glad to hear that."

John looked sharply at her. "She's working with replicators."

"That may be so, but my dear friend is not dead as I had thought, so I live with hope now that you can bring her home."

John looked away. "We'll have to see about that." He said, voice hard, but not angry as it had sounded before.

"Does she not want to come back to Atlantis?"

"I don't know, Teyla. But I promise I'll do everything I can to get her home."

"I know. Of that I am sure, John."

John nodded and left.

* * *

Rodney and Radek were just on their way out of the latter's lab when Sam buzzed in on Rodney's radio.

"McKay, do you have a minute?"

"Sam? Uh, is it important?" It hadn't quite sounded like it could wait.

He heard her breathe in deeply. "Yes."

"Uh, ok then, you need me in your office?"

"Yes. See you in a few." She signed off.

Rodney handed the scanner he was holding to the Czech, who already had several pieces of technology on his arms. "Ok, just put this with the rest."

"Yes, Rodney." He said, sounding as if he'd said it many times already.

When Rodney got to Carter's office he noticed she was very agitated. She was pacing the room, eyes boring into the floor.

"What's the matter?" he asked.

Her head snapped up. "Oh I just got off from a conversation with Mr. Coolidge. The IOA always knows how to rattle you." She laughed ruefully.

"They approved the mission right?"

"Yes they did." She leaned against the desk before adding, "I didn't tell them about Dr. Weir."

"Oh."

"Yeah, well the mission is approved, but…"

"But?" Rodney prompted.

She still hesitated.

"Come on Sam, I am the only scientist around here that gets to build up the suspense over bad news. But what?" he sounded slightly impatient.

Sam locked eyes with him. "When you're done you have orders to destroy them all. Can you do that?"

Rodney looked at her in a little surprise, though he supposed he should have seen that coming.

"Uh, if need be I can come up with something on the ship, but, yes, I believe so."

"Good." Rodney sensed that that wasn't all she had to say. And apparently this was the bad part, the part that had caused her to be so nervous and reluctant. She seemed to brace herself and finished. "Unless you can find a way to help Dr. Weir with her nanites, Rodney, destroying them includes her as well."

Rodney's face took on a stricken look. "But-"

She didn't give him a chance to speak. "Those are your orders McKay."

She said it but she looked uncomfortable. "It's up to you whether or not you tell Colonel Sheppard. If he's angry, I'll deal with him."

Rodney nodded reluctantly, and for a moment he looked completely lost.

She cleared her throat. "McKay, you're a brilliant person, you know a lot about these nanites. I'm sure you'll find a way to help her."

He took on one of his smaller annoyed looks, but couldn't hide from Sam that he was in fact hiding what he felt; scared.

"Of course I will." He said. "And now if you'll excuse me, I need to go make sure Zelenka didn't ruin anything in my lab. We need to leave soon."

She nodded and followed him down through the control room. In the back of her mind she silently hoped that, if worse came to worse and he couldn't figure out Elizabeth's nanite programming, that he would disobey orders to save her – exactly like he had before.


	6. Chapter 6

**A/N (saphire): **Thank you to everyone who reviewed! Took a little longer than a week to post, but I hope enjoy chapter 6! Please keep on reading and reviewing. I love to hear what you all think!

**A/N (shimmer):** Sorry about taking a little longer to update this one, but here's the next chapter! Thanks for all the reviews so far, don't forget on this chapter! And the next one will defibately have some Sparky written by me.

* * *

Chapter 6

"You ready to leave, McKay?" John called to the back of the jumper.

Rodney finished putting something in one of the many boxes stacked up. "Almost." Shutting the lid, he made his way to the copilot's seat. "Ok. Ready."

"Sam? We're ready to go," John said into his radio.

"All right. You have a go." She signaled for Chuck to open the retractable roof.

Teyla stood by Sam. "Good luck," she told them.

"Thanks. Don't have the baby while we're gone."

Teyla smiled slightly. "I am hardly close enough, John."

"Yeah, well, see you in a week, I guess." With that they flew off.

"Yeah." Sam sighed. It had been a surprise when John had told her that they would be gone for a week. Apparently he had 'forgotten' to mention it during the briefing room. She doubted that though as he had waited until they were finished up loading the jumper to say anything.

She still wasn't sure how she was going to tell General Landry that Atlantis' main team was going to be gone for a week. She hoped nothing serious happened to them while with the replicators. She also hoped nothing serious happened on Atlantis in that time. _Well, _she thought, _at least we have Major Lorne's team._

* * *

The door to John's room opened and he walked in. He found it very strange that they had normal bedrooms as he didn't think they ever had to sleep. He was even more disturbed when he realized the room was an exact replica of the quarters on Atlantis, just a bit smaller. But then again, they were created by the Ancients, the people who had built Atlantis and the replicators themselves had built two cities as of now.

At least he wasn't a prisoner anymore. That being said, there were two replicators that had showed him his room and were now standing just outside the door. He knew they'd been ordered to follow him wherever he went. It hurt slightly that Elizabeth wasn't trusting him, but he knew he'd do the same in her position.

As he put his belongings down he wondered how Ronon was doing. He knew Rodney had been taken to a lab where the research that had already been done on the weapon was being shown to him. So he wasn't really worried. But he didn't know about his Satedan friend. He had just been told that Ronon had also been assigned quarters on the ship.

He could picture the man sitting in his room, glaring at his 'babysitters' through the door. John decided he better go check on him. He sighed. He had a horrible feeling about this mission.

He walked back to the door and addressed the two there.

"You wouldn't happen to know where Ronon's room is, would you?" Nothing was said in response, though one of them, who he recognized as Dolan – unfortunately – started walking, clearly meaning him to follow. He did so and could feel the other one's eyes burning into his back the whole time.

As soon as the door started to open, Ronon was on his feet. When the caller turned out to be John, he relaxed but didn't sit back down. The door shut again.

"Hey buddy. How are you doin'?"

Ronon didn't answer the question. "Why do they have to be out there?" He asked instead, angrily indicating towards their guards.

"I'm sure it's just a precaution. I don't like a bunch of nanite robots watching us any more than you do, but we'd do the same in her position." He didn't like the way that sounded. Elizabeth herself was half replicator. As soon as this mission with the weapon was done he was putting Rodney on task about what to do with her nanites.

Ronon just grunted, telling John that he understood, but strongly disagreed.

"Where's McKay?" He changed the subject.

"They're showing him the data they've already got on the weapon."

They were silent for a moment. "I don't like this." Ronon stated finally.

"Me neither, big guy, but we don't have much of a choice. Besides, we're gonna get a whole lot of wraith dead out of this." He tried with a smile.

Ronon just grunted again.

* * *

Elizabeth sat in the captain's chair of the ship staring out through the glass that gave a full view of the blackness all around. Zarem sat at the controls next to her. She saw him glance nervously at her out of the corner of her eye. "Are you all right, Elizabeth?" he finally asked her.

"Why can we feel emotions, Zarem?" She suddenly asked, surprising him. "We're machines."

"The rest of us may be, but you are not. You know this. You are only half replicator."

"But you're full replicator and you can still feel emotions," she pointed out.

"Yes, I can. But I don't think I can give you any explanation as for why, Elizabeth."

She sighed and said nothing.

"Why did you ask?"

"Because sometimes I think it would just be easier not to feel anything. There would be no pain, no hurt, no sadness."

"But if you did not feel, then there wouldn't be any joy, happiness, love, excitement, or hope, either. There are many more positive emotions than negative and I believe that it is worth going through the negative ones to get the good."

Elizabeth looked at him. "Do you think I can get to the good emotions?"

"Yes, Elizabeth."

They were quiet again.

"If I may ask, what was this brought on by? The arrival of your friends?"

"Yes, Zarem. I think it was."

Maybe it would make you feel better to talk to them?" he suggested.

She nodded. "I think I'll go see Rodney first." She stood up and walked away towards the lab Rodney was in.

Zarem watched his half human friend depart, wishing that this had never happened to her.

* * *

Rodney was too engrossed in the files on the screen in front of him to notice Elizabeth's entrance when she reached the lab. "Rodney," she called his name to get his attention.

It did the trick. He whirled around. "Elizabeth." He wasn't quite sure if he was happy to see her or not.

"I came to see how you were doing."

"Oh. . . um. . . I'm doing fine." He turned to go back to the screen and caught sight of one of the replicator guards he had momentarily forgotten were in the room. "Are they really necessary?"

She smiled slightly, albeit a little sadly. "Yes, Rodney. They are. It's not that I don't trust you, it's just-"

"No, no it's fine. I understand." He read a few more lines of data before he sighed. There seemed to be a lot of sighing going around.

"Listen, Elizabeth. Teyla told me what you said about activating your nanites being a bad idea. I know what you went through last time, well actually I don't, but you know what I mean. I wouldn't purposely put you through that again and I just, um, wanted to, um, apologize. It was my fault. John was against it the whole time and I went behind his back. So I'm sorry."

Elizabeth let him ramble on until he was finished, knowing he needed to get out what he wanted to say. She saw pain and guilt written on his face. "Rodney, I don't blame you." She looked straight into his eyes, making sure he understood. "And you shouldn't blame yourself either. I understand what you were trying to do."

"I just couldn't sit back and watch you die. Not when I knew I could do something about it, Elizabeth."

"I know, Rodney. I know. And thanks."


	7. Chapter 7

**AN (sparkly):** hello again! Here's the next chapter, I think I got in some good Sparkyness (err...sorry, its uh, kinda angsty i suppose. But you all like that right?) You can be the judge of that. Thanks for the reviews so far, please let us know what you think of this part. Next bit should be up sooner than this one :)

**AN (saphire): **There's some Sparky in this chapter. Not much, but more will come in later chapters. As usual, thanks to everyone who reviewed! Let us know what you think of this chapter, please! Hope you like it.

Chapter 7

As Elizabeth left Rodney's room she debated with herself about going to see John. Her talk with Rodney had obviously cleared his mind some, but it hadn't helped her much. Although Ronon was a part of her… old family, he wasn't exactly the most open of people and they had never been close. So that left John. But he was a road block. He was different form when they had last seen each other almost a year ago. Things were going to be strained with him, she could tell. She could only hope they'd get over that. Right now was a time when she missed Teyla incredibly.

Biting her lip she decided she might as well try to talk with John. But when she knocked on his door he didn't answer. She could connect to the replicator collective to find out where they were but she quickly threw that idea away. She hated being connected. It only reminded her of that last mission and it made her feel even less human than she already was.

So instead Elizabeth quickly made her way to Ronon's room figuring he might be there. Hopefully they could get rid of some of the tension holding between them. She knocked on the door after dismissing the guards and some moments later the door opened. She faced a gruff Ronon.

She gave him a small smile and said, "Uh, hi Ronon, I was just looking for John…"

"What'd you need?" John asked coming from behind the larger man.

Elizabeth looked at him suddenly at a loss for words. As she stared she could only think of every time she had talked to him when he was unhappy about a mission. Every time he had had that slight look of defeat hiding in his eyes. She had always tried and usually succeeded at getting out of him why he was bothered. Sometimes they had talked in her office. A lot of the times had been for hours on the balcony.

And right now she recognized the look that was somewhere in his face. He was troubled and this time she thought sadly she doubted she could help. She was probably the reason for his distress. But if she thought about it, he looked like he'd been haunted by nightmares for a while now.

_That must be why he seems different to me. He's not as light-hearted. _And that thought broke her heart. She had always counted on him to make her smile. _Even Rodney and Ronon have that look about them. _She had to wonder what all had happened since her unceremonious departure.

"Elizabeth?" John's voice brought her out of her small reverie. But she still didn't know what to say. Why had she come again? Oh yeah, to talk with him. She wasn't sure she wanted to now.

She cleared her throat. "I wanted to tell you that I'll need to see you and Ronon and Rodney on the bridge in a few hours."

John looked closely at her sensing it indeed wasn't the reason she came. Apparently he decided to make light of the situation. "So we get to see you on your big commander's chair. Nice. But the Ancient chair is way cooler you know." He smiled and though it was somewhat strained it was genuine.

Elizabeth chuckled softly. "If you say so, Colonel. I didn't tell Rodney, so if you could let him know."

"No problem." She had let them keep their radios to contact each other.

"You may have to drag him away from the files we gave him."

"No problem." This time it came from Ronon.

She smiled at him briefly, slightly amused, and then turned back to John. Their eyes locked for a bit until John once again broke the silence.

"Anything else?"

She shook her head. "No." she said. "No that's it." However she still did not move, wanting desperately to stay in his company, even though he wasn't the same. It was still comforting knowing he was there. Looking for something to say her eyes noticed the apparently new Atlantis military uniforms.

"I see I'm not the only one with a new outfit." She commented lamely.

John looked down to his clothes. "Uh, the sleeves, right. Ask Rodney." He muttered, rolling his eyes good naturedly at his friend who wasn't there. Then he smirked. "You definitely win in that." His eyes traveled quickly up and down her body before going back up to see her flushing cheeks.

_Damn this leather _Elizabeth thought. _I knew it was a bad idea._ But she gave him a wide smile.

"Glad you like it, Colonel." She said, and caught Ronon's entertained grin. This felt so much like their relationship was back to normal. "I'll see you two in two hours." With that she left before she dug herself deeper into this mess.

* * *

John watched her walk away before Ronon pulled him away from the door so he could shut it, not before getting in a glare at the guards that were back.

Ronon felt bad for John. It killed him when he had had to leave Elizabeth behind. In fact Ronon felt bad for pulling him along back to the jumper that day. And now she was back. But it wasn't anything John wanted. He knew John was suffering more than anyone because there had always been something there between them. That had always been obvious. Still was in fact. Her eyes had lit up a bit when they were teasing each other.

"You're both avoiding talking to each other." he stated to John.

"What?" John asked, feigning ignorance as he walked around the room picking random things up that Ronon had set out, and setting them back down skewed.

"You're both scared to talk about what's happened."

"Why should I be scared to talk to Elizabeth?"

"Because you're afraid of your own feelings. Because you're afraid she hates what you did. Because you're afraid that she's gonna hate you."

John just stared at him.

"But I don't think she will. You two need to talk. You're going to have to sooner or later."

* * *

Elizabeth sat down in the captain's chair upon reentering the bridge. Zarim noticed she didn't look much happier since they had last spoken. In fact, she looked worse. "Did you talk to your friends?" he asked her.

She turned to look into his warm brown eyes that were full of concern for her. She was grateful for her friendship with him. She could practically talk to him about anything and trusted him immensely. Her relationship with him was definitely unlike the relationship she had with any of the other replicators. Part of it was due to how he treated her as a person, not just a commander to take orders from.

"Sort of," she responded.

"Sort of?" he probed when she didn't elaborate any further.

She shrugged. "I talked to Rodney."

"What about John?"

For a second Elizabeth wondered why he didn't ask about Ronon too, but let it slide. "We technically spoke."

"But did you _really talk_?"

"No," she reluctantly admitted, knowing he would disapprove of that.

He frowned slightly. "You need to."

"I know."

For several minutes there was silence. Then Zarem spoke again. "You like him don't you?"

"What?" His question surprised her. "Who?"

"John."

"No!" she immediately denied.

Zarem gave her a disbelieving look, clearly letting her know he thought otherwise, but said nothing more.

* * *

John, Rodney and Ronon walked on to the bridge followed by their guards. Several different men and women were working at the consoles. John looked at Elizabeth sitting in the Captain's chair, legs crossed. She was talking to a dark-haired replicator.

He walked over and when he was standing in front of her he gave her a sloppy solute.

"Reporting as ordered, Commander Weir." he said jokingly.

Elizabeth merely rolled her eyes. She hadn't even thought about the fact that she was in charge of him again.

"So what did you need us for?" he asked.

Before she could answer Rodney jumped in. "And do I really need to be here? Because that stuff I was looking at…"

Ronon cuffed him on the back of the head and he shut up.

"You all should know what's going on. We're not far from the planet where the weapon is. From what I gathered from our scientists the weapon is on the planet but should rise up into space?" She looked at Rodney, who nodded in confirmation.

"Right, well, first we'll be passing pretty closely to another planet." She turned to the brown-haired guy next to her. "Zarem, how far are we?"

"We should be there in approximately eight hours."

"Be where, exactly?" John asked, looking at Zarem.

"The wraith planet."


	8. Chapter 8

**AN (sparklyshimmer): **Please forgive us for the wait on this chapter, at one point we had final exams to worry about. Hopefully this chapter makes up for it. We had quite the disagreement on this one. Hope it all makes sense, enjoy! And tell us what you think.

**AN (saphire): **I apologize for the wait too. As my sis said above, part of the reason was studying for finals. So this chapter was a little difficult to do, but we finally managed. Hope you all like it and please keep on reveiwing and tell us what you think!

Chapter 8

This was just great, exactly what John needed. Another startling proclamation that could only mean no good for them. He felt ready to go to the wall and bang his head on it. A few times for good measure.

Reigning in his annoyance and surprise – and he really shouldn't have been surprised – he asked calmly, "What do you mean by 'the wraith planet'?"

"While we've been working on our fight against the wraith we found out that they have cloning facilities. They're huge. They take DNA from a queen apparently."

"Yeah we know. We found one recently." Rodney said.

"Blew it up too," said John smugly.

Elizabeth smiled. "Good. Now this planet has the largest cloning facility the wraith have, and it's incredibly active."

"Well how do you know that?" Rodney interrupted.

"There was a lot of information on the computers for the weapon," Zarem informed him.

"It's going to take a lot of fire power to destroy this facility, more than this ship can give," continued Elizabeth.

"That's what this weapon is for, isn't it?" John asked.

"Yes, and unfortunately we have to pass the wraith planet to get to the weapon. We don't know if we'll be detected by them or not."

"We can't go off course for a bit?"

"No, that's the problem. The planet with the weapon is cloaked. It– "

Rodney interrupted again. "The _whole planet _is cloaked?"

"Yes, Rodney."

"That would take a massive amount of energy."

"Yes. It's a small planet so it doesn't require too much power. But to conserve the power it does need, it uncloaks when it shoots."

"Huh," he said, and then made a gesture for Elizabeth to continue.

"As I was saying, the planet is cloaked. It doesn't show up on the sensors at all. We discovered it the last time when we were approaching from the opposite direction and the weapon detected us. It tried to take us out, but missed us by a pretty good margin. Hence why it needs fixed. We haven't been able to make it actually hit its target. It's also only supposed to attack the wraith, not us. But that's not the point right now. The point is we only know that the planet is near the wraith planet."

"Are you telling me that we have to stay on a course you think is right so we can have it shoot at us?"

Elizabeth chuckled. "Well like I said John, It's going to miss."

"You sure about that?"

"Positive," Zarem reported, but John still looked worried.

"Don't trust us, John?" Elizabeth asked. The team all turned to face her, noticing she seemed annoyed, almost angry.

John looked decidedly awkward as he said, "No it's not that, it's just I'd really rather not take that chance."

"Well, I'm sorry."

There was a moment of silence.

"So we have to wait to blow up the wraith from there?" This came from Ronon, sounding not at all happy.

"Yes. We are doing what is needed to do that, and that does require some amount of patience." Elizabeth said. Then she cleared her throat and looked at John uncomfortably. "Colonel?"

He gave her a questioning look.

"Can I talk to you? Alone?"

He narrowed his eyes at her, unsure about what she could want. He had gathered that she was as ready as he was to have The Talk, which was about as ready as a sheep was to go into the wolf's woods. So what could _this _be about?

"Lead the way."

* * *

Neither John nor Elizabeth spoke until they reached her quarters.

"What's up?" he asked.

"John, there's something else you need to know."

_Damn, _he thought, _my head is gonna become good friends with the wall for sure now._

"Alright, what?"

"Ok, as replicators you know we're programmed to be aggressive, right?"

"Even you?"

"Yes, John, even me."

"How?"

"That's not important." She said harshly. "What does matter is that you understand what is going to happen."

He didn't say anything.

"You know that command code to make the replicators attack the wraith?"

"Of course, the one we turned on…that one's in you too?"

"John, my base code is the same as theirs. I'm just not full replicator."

"Right." He said, though he was still confused. "Did you 'merge' with them?"

She frowned. "Not exactly."

"Come on, Elizabeth! Give me more than that!" he burst out.

She rubbed her hands over her face, her normal gesture of frustration. She sat down on the bed. "It happened while I was still at Oberoth's disposal. But that's not what I need to talk to you about."

"Fine. What about that code?"

"It makes us more aggressive, even angrier. It's very hard for us to control, and it's going to show once we get close to that wraith planet."

John wasn't sure what to make of that.

"We feel other emotions along with this rage, but it's there all the time, and when we get close, it's gonna come to the forefront….it…it's horrible, the way I feel," she said disgustedly. "I hate that I feel ready to do anything to get what I want."

She looked ashamed and all John wanted to do was hold her close and tell her everything would be ok. It hurt that he couldn't. In fact he hadn't touched her at all in what felt like forever. Not that he had touched her a lot on Atlantis, but the casual brush of hands and arms had always sent a shiver down his spine.

"It can't be that bad can it?" he tried to smile reassuringly, but wasn't sure if he managed it.

Elizabeth shook her head sadly. "You think I'm different now, John? That my behavior is strange, going from normal to angry in seconds? Once it comes out I probably won't be myself at all for a bit."

"Ok, so, you'll snap at me more than I deserve. I think I can handle that."

"John, I mean it."

His eyes darkened, thinking about the last time she had said those exact words to him. It was in the isolation room when she made him promise not to hesitate on the kill switch.

She caught on to his change of mood and spoke her next words softly.

"All I'm saying, John, is it might be a little surprising. I don't think anything should happen, but, I'm apologizing in advance."

She left the room with that and John followed shortly, wondering what was going to happen.

* * *

Eight hours went by too fast in John's opinion. And now they were close to the wraith planet. Him and Ronon had spent the time in the lab where Rodney was, rather bored. There were two others working in there along with their guards.

John had informed his friends about what Elizabeth had told him. And for the last little while the three had noticed some changes with the group in the lab. They all seemed ready to use their weapons. One had snapped at Rodney, sounding, if possible, more arrogant than the Canadian scientist. Since then Rodney had not spoken a word to them and continued to look at the logs silently.

Ronon had chosen to engage on a glaring competition with one of his guards.

"Relax, McKay." John said as his friend glanced nervously over his shoulder at one of the men. "I don't think they're gonna suddenly start shooting at us."

"Yeah and when we first met them they were 'letting us go.'"

"We're working _with _them. They're just a bunch of grumps at the moment." He sounded confident, though inside he was a bit disturbed by the transition from smiles to anger.

Rodney just shook his head and stole another peek at Huron, standing over a console nearby.

Being bored out of his mind, and slightly nervous about Elizabeth, he decided to go check up on her. Better he see her first than either Ronon or McKay.

He made his way to where he eventually found her. She was sitting down at a table in a lab not currently being used. She was looking out the window that showed the space they were flying through.

"Hey," he said casually. His guard had thankfully decided he could do no harm in there at the moment, and stood outside the door.

When she looked up at him he was taken aback at the steeliness that had entered her eyes. He hesitated to sit down.

"What do you want, Colonel?" she sounded impatient.

"Er, well, I just came to, you know…talk…"

"About what?"

"Nothing in particular…"

"I don't feel like talking right now."

"Look, Elizabeth, we both know we need to talk about what happened." _Idiot! You say that _now_? _

"Not right now, John." Her eyes flashed.

_Alright, so maybe later is a good idea. _"But we will later?" he pressed softly.

She nodded shortly.

He took a moment to study her. Though her eyes seemed fierce, she also seemed sad and regretful. "You, uh, ok?"

She didn't respond. "Come one, Elizabeth! I still care about you. Please just talk to me. I want to know what the hell they did to you after I left." Damn he needed to tape his mouth shut. She had warned him.

She stood up angrily. "No."

"And why not?"

"You have no idea what I went through."

"Not unless you tell me." He implored.

"No," she said again.

_And maybe staple it for good measure_, he thought. He let out a breath in frustration.

"So they did more than just try to get information from you?"

"Are you kidding me, John? I was half-replicator because you activated my nanites! When you knew I didn't want you to, I might add. You don't think they were the least bit interested in that?" And without warning her hand shot up to sink into his forehead.


	9. Chapter 9

**A/N (Saphire): **So I know that everyone has had to wait an incredibly long time for this chapter. I wish I could blame school, (and I guess I partially can because this year has been crazy!) but I probably could have gotten this done sooner. And Puddle-Jumper38 had to bug us way more than she should have before I updated. The next chapter should hopefully not take almost a year! Anyway, this chapter is going off of Adrift and Lifeline. Not a lot of new stuff, but I promise that that is coming! I hope you like it!

**A/N (Shimmer): **So sorry for the long wait! I don't think we'll take as long for the next update. (Thank you Puddle-Jumper38 for bugging usenough to fininsh this chap! *squeezes*) We've got some good stuff coming I think, so stick with us, and I hope you enjoy the chapter! Let us know what you think.

Chapter 9

John felt excruciating pain as Elizabeth's hand sank into his head. Then all of a sudden, the pain disappeared. He hesitantly opened his eyes. He was still in the lab on the ship, though the room was now empty and eerily silent. Elizabeth stood across from him, her expression none too pleasant.

Since she was already in his head and knew everything he was thinking, John figured attempting to not say anything that would set Elizabeth off was unnecessary. He had obviously already set her off.

"Ok, for the record, I am not the one who reactivated your nanites! Rodney was."

"But you were in charge, John! You could have stopped him! You _should _have stopped him!"

John was surprised. Just what exactly had she gone through to make her resent everything they did? "No! No, I couldn't have. He did it against my wishes! You know that! And you know what else? I'm glad he did. We'd never have saved Atlantis if we didn't get that ZPM. We'd never have gotten that ZPM if it wasn't for you. And I'd never have gotten to see your or, or talk to you again if Rodney hadn't done what he did." His voice gradually softened as he spoke.

Elizabeth's voice level lowered as well. "John, you have no idea what I went through during that mission. You have no idea just how horrified I was when I found out that my nanites were reactivated." She looked at him with pain in her eyes and he looked back with sorrow and some regret in his. "But you will."

John looked at her in confusion.

"I'm going to show you exactly what it was like for me."

Before John could say or ask anything, his surroundings started to fade away and slowly they morphed into the operating room on Atlantis. Elizabeth faded away too until she was replaced by another Elizabeth. This Elizabeth was lying on a hospital bed and her head was bandaged. John knew immediately what he was seeing.

Elizabeth woke up and looked around, trying to orient herself. She was wearing a hospital gown and was in a bed in the OR. The many machines that were around her beeped.

Her attention was then drawn to near the door by a shout calling for Doctor Keller. One of the nurses was backing away in shock.

John watched as himself and Rodney entered the room, followed by Ronon and Jennifer.

"John?" she asked, confused.

As the confusion flooded her expression, it also flooded John's body. He realized that he was feeling exactly what she was feeling. _So this is what she meant, _John thought.

Elizabeth reached up and pulled the bandage off. "Rodney? What's going on?"

John's surroundings shifted again. It was later when Teyla was talking to her as Jennifer ran a scanner up and down Elizabeth's body, both women wearing Hazmat suits. The confusion thankfully went away, but was only replaced with overwhelming despair. John decided he would rather have the confusion.

"They shouldn't have done this," Elizabeth told Teyla.

"None of us wanted to lose you, Elizabeth," Teyla justified.

"And what happens if the nanites are able to contact the other Replicators?" Elizabeth pointed out.

Worry was now added to the despair that John felt.

"Rodney does not believe that is possible."

Elizabeth shook her head. "No, it's reckless."

"In my opinion, it is well worth the risk."

Elizabeth leaned forward. "You have no idea what I went through the last time. Believe me, this is a very bad idea."

The scene shifted. Elizabeth was still sitting on the bed and John, Rodney, Ronon and Teyla were there as well.

"The nanites inside you," Rodney explained, "I think if we got them in close proximity to the human-form Replicators' city, I'd be able to manipulate them to remotely hack into the Replicator mainframe."

"We'd be able to find out where the closest ZPM is and the quickest way to get in and out." John said.

"Not only that, we'd be able to track their movement as well," McKay added.

"We'll know they're coming before they can even spot us," Ronon said, further trying to convince Elizabeth.

"Which does not eliminate the danger," Teyla pointed out.

"Well, far from it, but…" McKay trailed off.

Teyla finished for him. "But it does give us a significant edge."

"What happens if the Replicators take control of the nanites inside me?" Elizabeth asked.

McKay tried to assure her, "Well, they won't. I would block any attempt – "

Elizabeth interrupted him. "But if they do?"

John's other self spoke. "I ordered Rodney to write a kill-switch into the nanites' code. If we trigger the program, it'll neutralize them."

Elizabeth lowered her head. "'Neutralize them.' You mean shut them off?"

McKay's voice was quiet when he next spoke. "Yes."

"And you said the nanites are all that are keeping me alive."

"They are," John's other self said, "If we shut them off, it will…kill you."

John remembered how hard that had been to say for him. The thought of losing Elizabeth was one he had tried to firmly push out of his mind – several times. But then he had ended up losing her. _I can't think about that, _John thought, _I found her again and I'm not going to let her go. I'll bring her home. I'll figure out something, _he promised himself.

His other self's voice softened. "But that is not gonna happen, alright? I've ordered Rodney to keep an eye on the little bastards, make sure they behave."

"We would not ask this of you if it was not the only chance of this mission succeeding," Teyla said.

"She's right. If we don't get hold of a ZedPM, this city and everyone in it are gonna – "

Elizabeth didn't give Rodney a chance to finish. She looked at the other John and asked, "When do we leave?"

John had been feeling scared, worried, nervous, tense, etc. and he believed that he was reliving the strong emotions he had felt at the moment before him so many months ago. That those feelings were overpowering Elizabeth's. But as Elizabeth spoke, he felt determination flow through him, and he knew that what he had been feeling were actually Elizabeth's emotions as well.

The other John looked right back at her. "Right now."

Rodney started freaking out. "What? Wait – no – no – no – no – no – no – no – no, not right now. Look, I haven't finished finalizing the power distri–"

The other John cut him off. "Finalize it – we need to move."

Rodney quieted and quickly left the room, Ronon and Teyla closely behind him. As the door closed, the other John walked closer to the bed.

"You're gonna be ok, Elizabeth."

She gave him a small smile, appreciating his effort to make her feel better. "Still, I would like all of you to keep a very close eye on me, and the first sign of any suspicious behavior, do not hesitate with that kill-switch."

"Ok, but that's not gonna happen…"

John felt Elizabeth's exasperation and frustration with the situation.

Elizabeth looked him straight into his eyes. "John, I mean it."

They stared at each other for a moment. Elizabeth nodded her head and the other John nodded back.

Then the scene started to shift again. The scene had been going on long enough, it took John a minute to realize what was going on.

Now he was seeing Elizabeth sitting in the jumper, directing the other John and Ronon through the Replicator's city. Immediate relief flowed through her (and John) as they returned to the jumper unharmed.

The scenes started to shift faster.

Elizabeth was giving more directions. "Now turn right."

A schematic of the Replicator city filled his view.

"Hurry, John," Elizabeth was saying. "They're coming – and there's hundreds of them."

"Oberoth is heading to the Core Room." She looked at Rodney. "He knows it's us."

Elizabeth opened the door to the jumper and ran out with McKay yelling after her. "Elizabeth! What are you doing?"

Oberoth turned a corner in the city and Elizabeth's hand shot into his forehead.

Oberoth was speaking. "You desire to protect your people is admirable. But you will ultimately fail."

And as each scene flashed by, the emotions came and went just as quickly. Apprehension, worry, fear, desperation, adrenalin, determination, anger.

Then the shifting slowed down.

John heard his own voice. "We're _not_ leaving you behind!"

"If you don't leave right now, _none _of us will get out of here, so _go_." She turned her head slightly towards him. "THAT'S AN ORDER!"

John didn't want to watch anymore. The emotion he felt this time was overwhelming. Extreme anguish and despair encompassed him. Elizabeth didn't want to be captured. But she knew there was no other way to save her people. And she would do anything she possibly could for them.

Her concentration was broken now. Oberoth dropped the hand he had been holding away from his forehead. A blast from behind shot forward. Ronon turned, reaching toward the other John in an attempt to get him moving.

"Come on!" Ronon shouted.

"Elizabeth!" the other John still refused to leave without her.

"Go!" Elizabeth turned and yelled at him as the now unfrozen Replicator's rushed forward. They surrounded her and seized her arms.

He had no choice but to turn and run with Ronon.

He felt satisfaction through radiating sadness that tightened his chest as he watched himself leave. Then the scene changed again, but all he saw for a brief moment was Elizabeth lying down in a cell, body shaking as if she was silently sobbing. There was a cascade of emotions and then suddenly everything quit.

The scene ended, fading away, and once again becoming the empty, silent lab on the ship. Elizabeth was standing in front of him.

The majority of the gut-wrenching emotion went away, but John was left reeling. Then came more pain. Elizabeth was removing her hand from his head.

He was back in the real world. He saw the Replicator who was guarding him further into the room, no doubt alarmed by Elizabeth's shouting. The other Replicator's in the lab appeared again too and he could hear the sounds of them working. His head was pounding, but he decided he would take that any day over the emotional torture he had just been put through.

He looked at Elizabeth. Her face had gone blank.

"Now you know what it was like for me," she said. Then without waiting for him to answer, she turned on her heel and left.


End file.
